Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940

Tetracycline and fluoroquinolone antibiotics contamination in agricultural soils fertilized long-term with chicken litter: Trends and ravages

We investigated the potential accumulation of tetracyclines (TCs) such as chlortetracycline (CTC), oxytetracycline (OTC) and doxycycline (DC), and fluoroquinolones (FQs) like enrofloxacin (ENR) and ciprofloxacin (CIP) in chicken litter and agricultural soils fertilized over short-term to long-term (<1-30 yrs) with chicken litter in a poultry hub for the first time from Tamil Nadu, India. CTC, OTC, DC, CIP, and ENR were detected in 46-92 % of the selected chicken litter samples, with mean levels ranging from 2.90 to 23.30 μg kg-1. Higher concentrations of TCs and FQs were observed in freshly collected chicken litter from poultry sheds than in those stockpiled in cultivated lands. CTC was the prevalent antibiotic in chicken litter. The overall occurrence, as well as the ecological risks of TCs and FQs, changed over a 30-yr period. The accumulation of veterinary antibiotics (VAs) (in μg kg-1) in short-term (>1 yr) to medium-term (1-3 yrs) chicken litter-fertilized soils reached a maximum of 11.60 for CTC, 6.50 for OTC, 0.80 for DC, 3.70 for CIP, and 3.60 for ENR, but decreased in long-term (10-30 yrs) fertilized soils. Ecological risk assessment revealed a Risk Quotient (RQ) of ≤0.10 for CTC, OTC, and DC in all soils, while an average risk (RQ >0.10-<1.0) was evident with CIP and ENR in short-term and medium-term fertilized soils. Antibiotic resistance genes (ARGs), including tetA, tetB, qnrA, qnrB and qnrS were detected in most of the chicken litter samples and litter-fertilized soils. Thus, it is critical to develop and adopt effective mitigation strategies before applying chicken litter in farmlands to decrease VAs and ARGs, reducing their associated risks to public health and ecosystems in India considering 'One Health' approach. Future investigations on the occurrence of other VAs and ARGs in soils fertilized with poultry litter at regional scale are required for effective risk mitigation of the widely used VAs.

Metagenomics uncovers microbiome and resistome in soil and reindeer faeces from Ny-Ålesund (Svalbard, High Arctic)

Research on the microbiome and resistome in polar environments, such as the Arctic, is crucial for understanding the emergence and spread of antibiotic resistance genes (ARGs) in the environment. In this study, soil and reindeer faeces samples collected from Ny-Ålesund (Svalbard, High Arctic) were examined to analyze the microbiome, ARGs, and biocide/metal resistance genes (BMRGs). The dominant phyla in both soil and faeces were Pseudomonadota, Actinomycetota, and Bacteroidota. A total of 2618 predicted Open Reading Frames (ORFs) containing antibiotic resistance genes (ARGs) were detected. These ARGs belong to 162 different genes across 17 antibiotic classes, with rifamycin and multidrug resistance genes being the most prevalent. We focused on investigating antibiotic resistance mechanisms in the Ny-Ålesund environment by analyzing the resistance genes and their biological pathways. Procrustes analysis demonstrated a significant correlation between bacterial communities and ARG/BMRG profiles in soil and faeces samples. Correlation analysis revealed that Pseudomonadota contributed most to multidrug and triclosan resistance, while Actinomycetota were predominant contributors to rifamycin and aminoglycoside resistance. The geochemical factors, SiO42- and NH4+, were found to significantly influence the microbial composition and ARG distribution in the soil samples. Analysis of ARGs, BMRGs, virulence factors (VFs), and pathogens identified potential health risks associated with certain bacteria, such as Cryobacterium and Pseudomonas, due to the presence of different genetic elements. This study provided valuable insights into the molecular mechanisms and geochemical factors contributing to antibiotic resistance and enhanced our understanding of the evolution of antibiotic resistance genes in the environment.

Optimizing entropy weight model to accurately predict variation of pharmaceuticals and personal care products in the estuaries and coasts of the South China

Pharmaceuticals and personal care products (PPCPs) have raised increasing concern worldwide due to their continuous release and potential hazards to the ecosystem and human health. This study optimized the entropy weight model (EW-WRSR) that combines entropy weight with multi-criteria decision analysis to investigate pollution patterns of PPCPs in the coasts and estuaries. The results revealed that occurrences of PPCPs from the 1940s to the present were consistent with using PPCPs, different types of human activities, and local urban development. This helped better understand the history of PPCP contamination and evaluate the uncertainty of EW-WRSR. The model predicted hotspots of PPCPs that were consistent with the actual situation, indicating that PPCPs mainly enter the nearshore ecosystem by the form of sewage discharge and residual aquaculture. This study can provide method that identifying highly contaminated regions on a global scale.

Regulation of Antibiotic Resistance Genes on Agricultural Land Is Dependent on Both Choice of Organic Amendment and Prevalence of Predatory Bacteria

Antibiotic resistance genes (ARGs) are widespread in the environment, and soils, specifically, are hotspots for microorganisms with inherent antibiotic resistance. Manure and sludge used as fertilizers in agricultural production have been shown to contain vast amounts of ARGs, and due to continued applications, ARGs accumulate in agricultural soils. Some soils, however, harbor a resilience capacity that could depend on specific soil properties, as well as the presence of predatory bacteria that are able to hydrolyse living bacteria, including bacteria of clinical importance. The objectives of this study were to (i) investigate if the antibiotic resistance profile of the soil microbiota could be differently affected by the addition of cow manure, chicken manure, and sludge, and (ii) investigate if the amendments had an effect on the presence of predatory bacteria. The three organic amendments were mixed separately with a field soil, divided into pots, and incubated in a greenhouse for 28 days. Droplet digital PCR (ddPCR) was used to quantify three ARGs, two predatory bacteria, and total number of bacteria. In this study, we demonstrated that the choice of organic amendment significantly affected the antibiotic resistance profile of soil, and promoted the growth of predatory bacteria, while the total number of bacteria was unaffected.

Direct evolution of an alkaline fungal laccase to degrade tetracyclines

A fungal laccase-mediator system capable of high effectively oxidizing tetracyclines under a wide pH range will benefit environmental protection. This study reported a directed evolution of a laccase PIE5 to improve its performance on tetracyclines oxidization at alkaline conditions. Two mutants, namely MutA (D229N/A244V) and MutB (N123A/D229N/A244V) were obtained. Although they shared a similar optimum pH and temperature as PIE5, the two mutants displayed approximately 2- and 5-fold higher specific activity toward the mediators ABTS and guaiacol at pHs 4.0 to 6.5, respectively. Simultaneously, their catalytic efficiency increased by 8.0- and 6.4-fold compared to PIE5. At a pH range of 5-8 and 28 °C, MutA or MutB at a final concentration of 2.5 U·mL-1 degraded 77 % and 81 % of 100 mg·L-1 tetracycline within 10 min, higher than PIE5 (45 %). Furthermore, 0.1 U·mL-1 MutA or MutB completely degraded 100 mg·L-1 chlortetracycline within 6 min in the presence of 0.1 mM ABTS. At pH 8.0, MutA degraded tetracycline and chlortetracycline following the routine pathways were reported previously based on LC-MS analysis.

Antibiotic resistance genes: A global change factor

This invited commentary paper discusses the concept of elevated antibiotic resistance genes as a global change factor.

Study on the creation of boronate affinity-based oriented imprinted silica nanoparticles and their selective recognition toward glycopeptide antibiotics in food and water

Taking into account the drug resistance of antibiotics, teicoplanin has been banned in the veterinary field. Also, it brings threat to people's health when they eat foods containing teicoplanin residue. In addition, the abuse of teicoplanin in humans and food animals also poses a potential risk to water. Therefore, it is crucial to purify teicoplanin from food before quantifying its amount. In this study, researchers employed boronate affinity-based controlled oriented surface imprinting technique to produce molecularly imprinted polymers (MIPs) for the isolation of teicoplanin. The 3-fluoro-4-formylphenylboronic acid-functionalized silica nanoparticle substrate was first used as the supporting material for immobilizing teicoplanin. Next, the substrate surface was coated with an imprinting coating whose thickness could be controlled, produced through the self-copolymerization of dopamine and m-aminophenylboronic acid (APBA) in water. After the template was removed, 3D cavities that matched the template were created in the imprinting layer. The prepared teicoplanin-imprinted silica nanoparticles exhibited several significant satisfactory results such as good specificity, high binding capacity (46.9 ± 2.3 mg g-1), moderate binding constant ((5.46 ± 0.18) × 10-5 M-1), fast kinetics (8 min) and low binding pH (pH 5.0) toward teicoplanin. The teicoplanin-imprinted silica nanoparticles could still be reused after seven cycles of adsorption-desorption, which indicated a high chemical stability. In addition, recoveries of the proposed method for teicoplanin at three spiked levels in milk and water ranged from 91.8 to 105.6% and 92.3 to 97.4%, respectively. The teicoplanin-imprinted silica nanoparticles are capable of identifying the target teicoplanin in real samples in a simple, fast, selective and efficient manner.

Effect of meddling ARBs on ARGs dynamics in fungal infested soil and their selective dispersal along spatially distant mycelial networks

During the recent times, environmental antibiotic resistance genes (ARGs) and their potential transfer to other bacterial hosts of pathogenic importance are of serious concern. However, the dissemination strategies of such ARGs are largely unknown. We tested that saprotrophic soil fungi differentially enriched antibiotic resistant bacteria (ARBs) and subsequently contributed in spatial distribution of selective ARGs. Wafergen qPCR analysis of 295 different ARGs was conducted for manure treated pre-sterilized soil incubated or not with selected bacterial-fungal consortia. The qPCR assay detected unique ARGs specifically found in the mycosphere of ascomycetous and basidiomycetous fungi. Both fungi exerted potentially different selection pressures on ARBs, resulting in different patterns of ARGs dissemination (to distant places) along their respective growing fungal highways. The relative abundance of mobile genetic elements (MGEs) was significantly decreased along fungal highways compared to the respective inoculation points. Moreover, the decrease in MGEs and ARGs (along fungal highways) was more prominent over time which depicts the continuous selection pressure of growing fungi on ARBs for enrichment of particular ARGs in mycosphere. Such data also indicate the potential role of saprotrophic soil fungi to facilitate horizontal gene transfer within mycospheric environmental settings. Our study, therefore, advocates to emphasize the future investigations for such (bacteria-fungal) interactive microbial consortia for potential (spatial) dissemination of resistance determinants which may ultimately increase the exposure risks of ARGs.

Critical insights into the Hormesis of antibiotic resistome in saline soil: Implications from salinity regulation

Soil is recognized as an important reservoir of antibiotic resistance genes (ARGs). However, the effect of salinity on the antibiotic resistome in saline soils remains largely misunderstood. In this study, high-throughput qPCR was used to investigate the impact of low-variable salinity levels on the occurrence, health risks, driving factors, and assembly processes of the antibiotic resistome. The results revealed 206 subtype ARGs across 10 categories, with medium-salinity soil exhibiting the highest abundance and number of ARGs. Among them, high-risk ARGs were enriched in medium-salinity soil. Further exploration showed that bacterial interaction favored the proliferation of ARGs. Meanwhile, functional genes related to reactive oxygen species production, membrane permeability, and adenosine triphosphate synthesis were upregulated by 6.9%, 2.9%, and 18.0%, respectively, at medium salinity compared to those at low salinity. With increasing salinity, the driver of ARGs in saline soils shifts from bacterial community to mobile gene elements, and energy supply contributed 28.2% to the ARGs at extreme salinity. As indicated by the neutral community model, stochastic processes shaped the assembly of ARGs communities in saline soils. This work emphasizes the importance of salinity on antibiotic resistome, and provides advanced insights into the fate and dissemination of ARGs in saline soils.

Comparing Methods to Genetically Engineer Bacteriophage and Increase Host Range

INTRODUCTION

Antibacterial resistance is an emerging problem in military medicine. Disruptions to the health care systems in war-torn countries that result from ongoing conflict can potentially exacerbate this problem and increase the risk to U.S. forces in the deployed environment. Therefore, novel therapies are needed to mitigate the impact of these potentially devastating infections on military operations. Bacteriophages are viruses that infect and kill bacteria. They can be delivered as therapeutic agents and offer a promising alternative to traditional antibiotic chemotherapy. There are several potential benefits to their use, including high specificity and comparative ease of use in the field setting. However, the process of engineering phages for military medical applications can be a laborious and time-consuming endeavor. This review examines available techniques and compares their efficacy.

MATERIALS AND METHODS

This review evaluates the scientific literature on the development and application of four methods of bacteriophage genome engineering and their consideration in the context of military applications. Preffered Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed for a systematic review of available literature that met criteria for analysis and inclusion. The research completed for this review article originated from the United States Military Academy's library "Scout" search engine, which compiles results from 254 available databases (including PubMed, Google Scholar, and SciFinder). Particular attention was focused on identifying useful mechanistic insight into the nature of the engineering technique, the ease of use, and the applicability of the technique to countering the problem of antimicrobial resistance in the military setting.

RESULTS

A total of 52 studies were identified that met inclusion criteria following PRISMA guidelines. The bioengineering techniques analyzed included homologous recombination (12 articles), in vivo recombineering (9 articles), bacteriophage recombineering of electroporated DNA (7 articles), and the CRISPR-Cas system (10 articles). Rates of success and fidelity varied across each platform, and comparative benefits and drawbacks are considered.

CONCLUSIONS

Each of the phage engineering techniques addressed herein varies in amount of effort and overall success rate. CRISPR-Cas-facilitated modification of phage genomes presents a highly efficient method that does not require a lengthy purification and screening process. It therefore appears to be the method best suited for military medical applications.

Elevated levels of antibiotic resistance genes as a factor of human-caused global environmental change

Antibiotic resistance genes (ARGs) have moved into focus as a critically important response variable in global change biology, given the increasing environmental and human health threat posed by these genes. However, we propose that elevated levels of ARGs should also be considered a factor of global change, not just a response. We provide evidence that elevated levels of ARGs are a global change factor, since this phenomenon is linked to human activity, occurs globally, and affects biota. We explain why ARGs could be considered the global change factor, rather than the organisms containing them; and we highlight the difference between ARGs and the presence of antibiotics, which are not necessarily linked since elevated levels of ARGs are caused by multiple factors. Importantly, shifting the perspective to elevated levels of ARGs as a factor of global change opens new avenues of research, where ARGs can be the experimental treatment. This includes asking questions about how elevated ARG levels interact with other global change factors, or how ARGs influence ecosystem processes, biodiversity or trophic relationships. Global change biology stands to profit from this new framing in terms of capturing more completely the real extent of human impacts on this planet.

Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria

The co-selective pressure of heavy metals is a contributor to the dissemination and persistence of antibiotic resistance genes in environmental reservoirs. The overlapping range of antibiotic and metal contamination and similarities in their resistance mechanisms point to an intertwined evolutionary history. Metal resistance genes are known to be genetically linked to antibiotic resistance genes, with plasmids, transposons, and integrons involved in the assembly and horizontal transfer of the resistance elements. Models of co-selection between metals and antibiotics have been proposed, however, the molecular aspects of these phenomena are in many cases not defined or quantified and the importance of specific metals, environments, bacterial taxa, mobile genetic elements, and other abiotic or biotic conditions are not clear. Co-resistance is often suggested as a dominant mechanism, but interpretations are beset with correlational bias. Proof of principle examples of cross-resistance and co-regulation has been described but more in-depth characterizations are needed, using methodologies that confirm the functional expression of resistance genes and that connect genes with specific bacterial hosts. Here, we comprehensively evaluate the recent evidence for different models of co-selection from pure culture and metagenomic studies in environmental contexts and we highlight outstanding questions.

The impacts of animal agriculture on One Health-Bacterial zoonosis, antimicrobial resistance, and beyond

The industrialization of animal agriculture has undoubtedly contributed to the improvement of human well-being by increasing the efficiency of food animal production. At the same time, it has also drastically impacted the natural environment and human society. The One Health initiative emphasizes the interdependency of the health of ecosystems, animals, and humans. In this paper, we discuss some of the most profound consequences of animal agriculture practices from a One Health perspective. More specifically, we focus on impacts to host-microbe interactions by elaborating on how modern animal agriculture affects zoonotic infections, specifically those of bacterial origin, and the concomitant emergence of antimicrobial resistance (AMR). A key question underlying these deeply interconnected issues is how to better prevent, monitor, and manage infections in animal agriculture. To address this, we outline approaches to mitigate the impacts of agricultural bacterial zoonoses and AMR, including the development of novel treatments as well as non-drug approaches comprising integrated surveillance programs and policy and education regarding agricultural practices and antimicrobial stewardship. Finally, we touch upon additional major environmental and health factors impacted by animal agriculture within the One Health context, including animal welfare, food security, food safety, and climate change. Charting how these issues are interwoven to comprise the complex web of animal agriculture's broad impacts on One Health will allow for the development of concerted, multidisciplinary interventions which are truly necessary to tackle these issues from a One Health perspective.

Comparative Study of Systemic vs. Local Antibiotics with Subgingival Instrumentation in Stage III-IV Periodontitis: A Retrospective Analysis

To improve the clinical and microbiological outcomes of non-surgical mechanical periodontal therapy, the adjunctive use of antimicrobials has been utilized in treating moderate-to-severe periodontitis. In our study, the retrospective design included previously collected health-related patient data, obtained from the printed and digital charts of patients who received systemic or local antibiotic adjuncts to SI (subgingival instrumentation). A total of 34 patients (diagnosed with generalized Stage III/IV periodontitis) met the inclusion and exclusion criteria and were evaluated. The samples were tested for the following bacterial strains: Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans), Porphyromonas gingivalis (P. gingivalis), Prevotella intermedia (P. intermedia), Tanererella forsythia (T. forsythia), and Treponema denticola (T. denticola). The inter-group comparisons of the bacterial species did not show statistically significant differences between groups. The present study aimed to evaluate the clinical effects after SI and the adjunctive use of systemically administered (SA) AMX (amoxicillin) + MET (metronidazole) (administered for 7 days), with locally delivered (LDD) piperacillin + tazobactam in step 2 of periodontal therapy. Results: Overall, all parameters were improved in the groups, with a significant difference in inter-group comparison regarding the full-mouth bleeding score (FMBS) (p < 0.05) in favor of the SA group, and the p-value < 0.05 was considered to be statistically significant. Statistically significant PPD (probing pocket depth) reductions and CAL (clinical attachment level) gains were observed in both groups at the 3-month follow-up. In conclusion, within the limitations, the outcomes of this study suggest that SI, with adjunctive local or systemic antibiotic therapy, provided comparable clinical improvements. Systemic AMX + MET protocols were more efficacious with regard to the reduction in FMBS. Follow-up studies with larger patient numbers are needed to further investigate this effect.

Triazole resistance in Aspergillus fumigatus isolated from a tomato production environment exposed to propiconazole

The emergence of azole-resistant Aspergillus fumigatus (ARAf) across the world is an important public health concern. We sought to determine if propiconazole, a demethylase inhibitor (DMI) fungicide, exerted a selective pressure for ARAf in a tomato production environment following multiple exposures to the fungicide. A tomato field trial was established in 2019 and propiconazole was applied weekly until harvest. Soil, leaf, and fruit (when present) samples were collected at baseline and after each propiconazole application. A. fumigatus isolates (n, 178) were recovered and 173 were tested for susceptibility to itraconazole, posaconazole, voriconazole, and propiconazole in accordance with CLSI M38 guidelines. All the isolates were susceptible to medical triazoles and the propiconazole MIC ranged from 0.25 to 8 mg/L. A linear regression model was fitted that showed no longitudinal increment in the log2-fold azole MIC of the isolates collected after each propiconazole exposure compared to the baseline isolates. AsperGenius real-time multiplex assay ruled out TR34/L98H and TR46/Y121F/T289A cyp51A resistance markers in these isolates. Sequencing of a subset of isolates (n, 46) demonstrated widespread presence of F46Y/M172V/E427K and F46Y/M172V/N248T/D255E/E427K cyp51A mutations previously associated with reduced susceptibility to triazoles.

IMPORTANCE

The agricultural use of azole fungicides to control plant diseases has been implicated as a major contributor to ARAf infections in humans. Our study did not reveal imposition of selection pressure for ARAf in a vegetable production system. However, more surveillance studies for ARAf in food crop production and other environments are warranted in understanding this public and One Health issue.

Current examining methods and mathematical models of horizontal transfer of antibiotic resistance genes in the environment

The increasing prevalence of antibiotic resistance genes (ARGs) in the environment has garnered significant attention due to their health risk to human beings. Horizontal gene transfer (HGT) is considered as an important way for ARG dissemination. There are four general routes of HGT, including conjugation, transformation, transduction and vesiduction. Selection of appropriate examining methods is crucial for comprehensively understanding characteristics and mechanisms of different HGT ways. Moreover, combined with the results obtained from different experimental methods, mathematical models could be established and serve as a powerful tool for predicting ARG transfer dynamics and frequencies. However, current reviews of HGT for ARG spread mainly focus on its influencing factors and mechanisms, overlooking the important roles of examining methods and models. This review, therefore, delineated four pathways of HGT, summarized the strengths and limitations of current examining methods, and provided a comprehensive summing-up of mathematical models pertaining to three main HGT ways of conjugation, transformation and transduction. Finally, deficiencies in current studies were discussed, and proposed the future perspectives to better understand and assess the risks of ARG dissemination through HGT.

Antibiotic resistance genes and mobile genetic elements in different rivers: The link with antibiotics, microbial communities, and human activities

Rivers as a critical sink for antibiotic resistance genes (ARGs), and the distribution and spread of ARGs are related to environmental factors, human activities, and biotic factors (e.g. mobile genetic elements (MGEs)). However, the potential link among ARGs, microbial community, and MGEs in rivers under different antibiotic concentration and human activities remains unclear. In this study, 2 urban rivers (URs), 1 rural-urban river (RUR), and 2 rural rivers (RRs) were investigated to identify the spatial-temporal variation and driving force of ARGs. The total concentration of quinolones (QNs) was 160.1-2151 ng·g-1 in URs, 23.34-1188 ng·g-1 in RUR, and 16.39-85.98 ng·g-1 in RRs. Total population (TP), gross domestic production (GDP), sewage, industrial enterprise (IE), and IEGDP appeared significantly spatial difference in URs, RUR, and RRs. In terms of ARGs, 145-161 subtypes were detected in URs, 59-61 subtypes in RURs, and 46-79 subtypes in RRs. For MGEs, 55-60 MGEs subtypes were detected in URs, 29-30 subtypes in RUR, and 29-35 subtypes in RRs. Significantly positive correlation between MGEs and ARGs were found in these rivers. More ARGs subtypes were related to MGEs in URs than those in RUR and RRs. Overall, MGEs and QNs showed significantly direct positive impact on the abundance of ARGs in all rivers, while microbial community was significantly positive impact on the ARGs abundance in URs and RUR. The ARGs abundance in URs/RUR were directly positive influenced by microbial community/MGEs/socioeconomic elements (SEs)/QNs, while those in RRs were directly positive influenced by QNs/MGEs and indirectly positive impacted by SEs. Most QNs resistance risk showed significantly positive correlation with the abundance of ARGs types. Therefore, not only need to consider the concentration of antibiotics, but also should pay more attention to SEs and MGEs in antibiotics risk management and control.

Sequence-structure-function characterization of the emerging tetracycline destructase family of antibiotic resistance enzymes

Tetracycline destructases (TDases) are flavin monooxygenases which can confer resistance to all generations of tetracycline antibiotics. The recent increase in the number and diversity of reported TDase sequences enables a deep investigation of the TDase sequence-structure-function landscape. Here, we evaluate the sequence determinants of TDase function through two complementary approaches: (1) constructing profile hidden Markov models to predict new TDases, and (2) using multiple sequence alignments to identify conserved positions important to protein function. Using the HMM-based approach we screened 50 high-scoring candidate sequences in Escherichia coli, leading to the discovery of 13 new TDases. The X-ray crystal structures of two new enzymes from Legionella species were determined, and the ability of anhydrotetracycline to inhibit their tetracycline-inactivating activity was confirmed. Using the MSA-based approach we identified 31 amino acid positions 100% conserved across all known TDase sequences. The roles of these positions were analyzed by alanine-scanning mutagenesis in two TDases, to study the impact on cell and in vitro activity, structure, and stability. These results expand the diversity of TDase sequences and provide valuable insights into the roles of important residues in TDases, and flavin monooxygenases more broadly.

The need for One Health systems-thinking approaches to understand multiscale dissemination of antimicrobial resistance

Although the effects of antimicrobial resistance (AMR) are most obvious at clinical treatment failure, AMR evolution, transmission, and dispersal happen largely in environmental settings, for example within farms, waterways, livestock, and wildlife. We argue that systems-thinking, One Health approaches are crucial for tackling AMR, by understanding and predicting how anthropogenic activities interact within environmental subsystems, to drive AMR emergence and transmission. Innovative computational methods integrating big data streams (eg, from clinical, agricultural, and environmental monitoring) will accelerate our understanding of AMR, supporting decision making. There are challenges to accessing, integrating, synthesising, and interpreting such complex, multidimensional, heterogeneous datasets, including the lack of specific metrics to quantify anthropogenic AMR. Moreover, data confidentiality, geopolitical and cultural variation, surveillance gaps, and science funding cause biases, uncertainty, and gaps in AMR data and metadata. Combining systems-thinking with modelling will allow exploration, scaling-up, and extrapolation of existing data. This combination will provide vital understanding of the dynamic movement and transmission of AMR within and among environmental subsystems, and its effects across the greater system. Consequently, strategies for slowing down AMR dissemination can be modelled and compared for efficacy and cost-effectiveness.

D-Ring Modifications of Tetracyclines Determine Their Ability to Induce Resistance Genes in the Environment

The widespread utilization of tetracyclines (TCs) in agriculture and medicine has led to the borderless spread of tetracycline resistance in humans, animals, and the environment, posing huge risks to both the ecosystem and human society. Changes in the functional group modifications resulted in a higher bacteriostatic efficacy of the new generation of TCs, but their effect on the emergence and evolution of antibiotic resistance genes (ARGs) is not yet known. To this end, four TCs from three generations were chosen to compare their structural effects on influencing the evolution of ARGs in soil microbial communities. The findings revealed that low-generation TCs, such as tetracycline and oxytetracycline, exhibited a greater propensity to stimulate the production and proliferation of ARGs than did high-generation tigecycline. Molecular docking analysis demonstrated that modifications of the D-ring functional group determined the binding capacity of TCs to the substrate-binding pocket of transcriptional regulators and efflux pumps mainly involved in drug resistance. This can be further evidenced by reverse transcription-quantitative polymerase chain reaction quantification and intracellular antibiotic accumulation assessment. This study sheds light on the mechanism of the structural effect of antibiotic-induced ARG production from the perspective of compound-protein binding, therefore providing theoretical support for controlling the dissemination of antibiotic resistance.

Fate, risk and sources of antibiotic resistome and its attenuation dynamics in the river water-sediment system: Field and microcosm study

Antibiotic resistance genes (ARGs) in rivers have received widespread attentions. Deciphering the fate and spread mechanisms of ARGs in river system can contribute to the design of effective strategies for reducing resistome risk in the environment. Although some studies have reported the prevalence and distribution of ARGs in rivers worldwide, few have systematically explored their fates, sources and risks in river water-sediment system. Also, the role of natural sunlight on the attenuation and fate of ARGs in river remains to be demonstrated. To fill the gaps, field investigation and microcosm experiment have been conducted in this study to reveal the fate, risk, source-sink relationship and attenuation dynamics of ARGs in an urban river water-sediment system, by utilizing high-throughput sequencing-based metagenomic assembly analysis and machine-learning-based source tracking tool. In all, 527 unique ARGs belonging to 29 antimicrobial classes were identified in the river. Relatively, the level of ARGs in the sediments were significantly higher (p < 0.05) than that in the waters. Variance partitioning analysis indicated the biotic and abiotic factors co-governed the riverine resistome, totally explaining 76% and 83% variations of ARGs in the waters and sediments, respectively. Microcosm experiment under natural light and dark condition showed that light induced the decay of ARGs in the waters and might promote their transfers from waters to sediments, which were also confirmed by the attenuation dynamics of bacteria in the experimental water-sediment system. Notably, the co-occurrences of ARGs with MGEs and VFs on the same contigs suggested resistome risk in the river, and relatively, the risk scores in the sediments were significantly higher (p < 0.05) than those in the waters. Source apportionment with metagenomic resistome signatures showed the Wenyu River was the most dominant contributor of ARGs in the downstream, with average contributions of 44.5% and 40.8% in the waters and sediments, respectively.

Emergence and mobilization of a novel lincosamide resistance gene lnu(I): From environmental reservoirs to pathogenic bacteria

Antimicrobial resistance remains an utmost concern in human and veterinary medicine, impacting humans, animals, and the environment while significantly influencing the principles of One Health. While Riemerella anatipestifer (R. anatipestifer) is recognized as a waterfowl pathogen with multidrug-resistant properties, the specifics of its lincosamide resistance mechanism are inadequately understood. In this study, we identified a novel lincosamide resistance gene, lnu(I), in R. anatipestifer RCAD0121, and investigated its potential origin, transfer mechanisms, and dissemination status through genomic epidemiology. This exhibited 74.80 % amino acid identity with a previously reported gene, lnu(H). PCR analysis revealed lnu(I) prevalence in at least 44 R. anatipestifer isolates collected from multiple provinces in China. Furthermore, genomic mining unveiled 56 lnu(I) sequences within publicly available databases, primarily originating from environmental sources. In addition, members of the family Flavobacteriaceae were the dominant (16/56, 28.57 %) bacteria carrying the lnu(I) gene, with Flavobacterium exhibiting a similar GC content as lnu(I). Notably, specific instances of the lnu(I) gene were linked to mobile genetic elements within human and animal pathogenic bacteria. These findings suggest that Flavobacterium species within the environment could serve as potential ancestral sources of the novel lnu(I) gene, which has undergone mobilization events toward pathogenic bacteria.

Transfer of antibiotic resistance genes from soil to wheat: Role of host bacteria, impact on seed-derived bacteria, and affecting factors

The transfer of antibiotic resistance genes (ARGs) from soils to plants is poorly understood, especially the role of host bacteria in soils and its impact on seed-derived bacteria. Wheat (Triticum aestivum L.) was thus used to fill the gap by conducting pot experiments, with target ARGs and bacterial community analyzed. Results showed that the relative abundances of target ARGs gradually decreased during transfer of ARGs from the rhizosphere soil to root and shoot. Host bacteria in the rhizosphere soil were the primary source of ARGs in wheat. The 38, 21, and 19 potential host bacterial genera of target ARGs and intI1 in the rhizosphere soil, root, and shoot were identified, respectively, and they mainly belonged to phylum Proteobacteria. The abundance of ARGs carried by pathogenic Corynebacterium was reduced in sequence. During transfer of ARGs from the rhizosphere soil to root and shoot, some seed-derived bacteria and pathogenic Acinetobacter obtained ARGs through horizontal gene transfer and became potential host bacteria. Furthermore, total organic carbon, available nitrogen of the rhizosphere soil, water use efficiency, vapor pressure deficit, and superoxide dismutase of plants were identified as the key factors affecting potential host bacteria transfer in soils to wheat. This work provides important insights into transfer of ARGs and deepens our understanding of potential health risks of ARGs from soils to plants.

Spatio-temporal distribution and dynamics of antibiotic resistance genes in a water-diversion lake, China

The distribution and dynamics of antibiotic resistance genes (ARGs) in water-diversion lakes are poorly understood. In this study, two comparative in situ investigations of ARG profiles targeting water diversion (DP) and non-diversion periods (NDP) were conducted in Luoma Lake, a vital transfer node for the eastern route of the South-to-North Water Diversion Project in China. The results demonstrated significant spatiotemporal variations in ARG contamination and notable differences in the co-occurrence patterns of ARGs and bacterial communities between DP and NDP. Correlations among ARGs with the 16 S rRNA, and mobile genetic elements indicate that horizontal gene transfer (HGT) and vertical gene transfer (VGT) in NDP, but only HGT in DP, were the primary mechanisms of ARG proliferation and spread, implying that water diversion could be an essential control of the transfer pattern of ARGs in a lake environment. The null model analysis indicated that stochastic processes, with predominant driver of ecological drift in the lake mainly drove the assembly of ARGs. Partial least squares structural equation modeling was developed to analyze the causal effects of the factors in shaping ARG dynamics and identify the major driving forces in the DP and NDP.

Knowledge and Attitude toward Antibiotic Use and Identification of Financially Feasible Options to Curb the Spread of Antibiotics in Environment

A survey on antibiotic literacy in terms of the use and abuse of antibiotics to track and understand antibiotic consumption is crucial to optimize the use of antibiotics and minimizing antimicrobial resistance (AMR). Purposive random sampling, using the snow-ball questionnaire technique, was adopted to ensure that the respondents distributed across India, coming from rural and urban settings, were adolescents as well as adults and had completed at least the higher secondary school level of education. Respondents were divided into five subcategories. The questionnaire was distributed between April 2021 and July 2021, during the second COVID-19 wave in India. The survey questionnaire included 34 questions, comprising multiple-choice and 5-point Likert scale-type questions. This study composed of 972 respondents. Most respondents considered antibiotics safe and frequently failed to discriminate between the symptoms of bacterial and viral infections, most often leading to self-prescription. About 34% of the rural participants and 50% of the urban participants considered antibiotic resistance a serious health concern. Antibiotic prescriptions by the medical or paramedical practitioner were largely empirical. At least 95% of participants acknowledged having heard about antibiotics; nearly 20% of antibiotic consumption came from nonprescription users, while 30% had not completed their antibiotic therapy for a variety of reasons. Sixty-two percent consumed antibiotics to treat cold and flu symptoms. Results from the survey suggest the presence of a crucial gap between the respondents' perception of antibiotics and levels of information regarding antibiotic use and misuse. The present study may serve as a benchmark that strongly recommends a financially feasible policy, which includes educating society regarding the spread of AMR and its severe consequences by incorporating AMR into the curriculum at the levels of senior secondary school and higher education.

Interplay Between Antimicrobial Resistance and Global Environmental Change

Antibiotic resistance genes predate the therapeutic uses of antibiotics. However, the current antimicrobial resistance crisis stems from our extensive use of antibiotics and the generation of environmental stressors that impose new selective pressure on microbes and drive the evolution of resistant pathogens that now threaten human health. Similar to climate change, this global threat results from human activities that change habitats and natural microbiomes, which in turn interact with human-associated ecosystems and lead to adverse impacts on human health. Human activities that alter our planet at global scales exacerbate the current resistance crisis and exemplify our central role in large-scale changes in which we are both protagonists and architects of our success but also casualties of unanticipated collateral outcomes. As cognizant participants in this ongoing planetary experiment, we are driven to understand and find strategies to curb the ongoing crises of resistance and climate change.

Probing the effects of streptomycin on Brassica napus germination and assessing its molecular interactions using extensive molecular dynamics (MD) simulations

Antibiotics are chemical compounds that are used to treat and prevent disease in humans and animals. They have been used in animal feed for over 60 years and are widely used in industrial farming. Antibiotics can have negative environmental impacts, including the potential to contribute to the development of antibiotic-resistant organisms. They can enter the environment through various pathways, including the manufacturing process, the direct application of antibiotic-laden manure to fields, and through grazing animals. Antibiotics that are given to animals can be excreted from where they can enter soil and groundwater which enable their entry in plants. Streptomycin is an antibiotic that is used against a range of gram-positive and gram-negative bacteria, but its use has led to the development of antibiotic resistance in some pathogens. It has also been shown to have negative impacts on a range of plant species, including tobacco, tomato, and wheat. Although, the major effect of streptomycin on plant physiology have been studied, the molecular mechanisms at play are barely understood in plant body. In current study, we examined the impact of streptomycin on germination of Brassica napus and then using docking, MM-GBBSA and MD simulations identified key proteins that interact with streptomycin by performing rigorous computational screening of 106 different proteins. Our finding suggest that streptomycin might be interacting with acyl-CoA oxidases, protochlorophyllide reductase B and leucoanthocyanidin dioxygenase based on simulation and docking analysis.

Wastewater treatment plant effluents exert different impacts on antibiotic resistome in water and sediment of the receiving river: Metagenomic analysis and risk assessment

Wastewater treatment plants (WWTPs) are considered as hotspots for the spread of antibiotic resistome into the environment. However, the differential contributions of WWTPs to the antibiotic resistome in the receiving river water and sediment are poorly understood. Here, based on metagenomic analysis, we found that the WWTP effluents significantly elevated the diversities and abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in the receiving river water from the Qinghai-Tibet Plateau, but showed less interference with the antibiotic resistome in sediment. Estimated by SourceTracker, WWTPs contributed 60.691.8% of ARGs in downstream river water, much higher than those for sediment (7.7568.0%). A holistic comparison of ARG risks based on analysis of ARG combination, mobility risk, ARG hosts and ARG-carrying pathogens further revealed the great impacts of WWTP effluents on downstream river water rather than sediment. Among various MGEs, tnpA exhibited the greatest potential for the dissemination of ARGs, and displayed highest co-occurrence frequency with multiple ARGs. P. aeruginosa, E. cloacae, and E. coli were identified as the critical-priority pathogens of ARG hosts. This study demonstrated the much greater impacts of WWTP effluents on the downstream water compared with sediment, which is significant for developing effective strategies to mitigate ARG risks.

The effects of antibiotic use on the dynamics of the microbiome and resistome in pigs

Antibiotics are widely used in pig farming across the world which has led to concerns about the potential impact on human health through the selection of antibiotic resistant pathogenic bacteria. This worry has resulted in the development of a production scheme known as pigs Raised Without Antibiotics (RWA), in which pigs are produced in commercial farms, but are ear-tagged as RWA until slaughter unless they receive treatment, thus allowing the farmer to sell the pigs either as premium priced RWA or as conventional meat. Development of antibiotic resistance in pig farming has been studied in national surveys of antibiotic usage and resistance, as well as in experimental studies of groups of pigs, but not in individual pigs followed longitudinally in a commercial pig farm. In this study, a cohort of RWA designated pigs were sampled at 10 time points from birth until slaughter along with pen-mates treated with antibiotics at the same farm. From these samples, the microbiome, determined using 16S sequencing, and the resistome, as determined using qPCR for 82 resistance genes, was investigated, allowing us to examine the difference between RWA pigs and antibiotic treated pigs. We furthermore included 176 additional pigs from six different RWA farms which were sampled at the slaughterhouse as an endpoint to substantiate the cohort as well as for evaluation of intra-farm variability. The results showed a clear effect of age in both the microbiome and resistome composition from early life up until slaughter. As a function of antibiotic treatment, however, we observed a small but significant divergence between treated and untreated animals in their microbiome composition immediately following treatment, which disappeared before 8 weeks of age. The effect on the resistome was evident and an effect of treatment could still be detected at week 8. In animals sampled at the slaughterhouse, we observed no difference in the microbiome or the resistome as a result of treatment status but did see a strong effect of farm origin. Network analysis of co-occurrence of microbiome and resistome data suggested that some resistance genes may be transferred through mobile genetic elements, so we used Hi-C metagenomics on a subset of samples to investigate this. We conclude that antibiotic treatment has a differential effect on the microbiome vs. the resistome and that although resistance gene load is increased by antibiotic treatment load, this effect disappears before slaughter. More studies are needed to elucidate the optimal way to rear pigs without antibiotics.

Partitioning and migration of antibiotic resistance genes at soil-water-air interface mediated by plasmids

The partitioning and migration of antibiotic resistance genes (ARGs) at the interfaces of soil, water, and air play a critical role in the environmental transmission of antibiotic resistance. This study investigated the partitioning and migration of resistant plasmids as representatives of extracellular-ARGs (eARGs) in artificially constructed soil-water-air systems. Additionally, it quantitatively studied the influence of soil pH, clay mineral content, organic matter content, and simulated rainfall on the migration of eARGs via orthogonal experiments. The findings revealed that the sorption equilibrium between eARGs and soil can be attained within 3 h, following the two-compartment first-order kinetic model. The average partition ratio of eARGs in soil, water, and air is 7:2:1, and soil pH and clay mineral content are identified as the main influencing factors. The proportion of eARGs migrating from soil to water and air is 8.05% and 0.52%, respectively. Correlation and significance analyses showed that soil pH has a significant impact on the soil-water and soil-air mobility of eARGs, while clay content affects the percentage of peaks during migration. Moreover, rainfall exerts a noticeable impact on the timing of peaks during migration. This study provided quantitative insights into the proportion of eARGs in soil, water, and air and elucidated the key factors influencing the partitioning and migration of eARGs from the perspectives of the sorption mechanism.

The effect of antibiotic usage on resistance in humans and food-producing animals: a longitudinal, One Health analysis using European data

This paper estimates the effect of antibiotic usage in humans and food-producing animals on the prevalence of resistance in zoonotic bacteria in both humans and animals. Using comprehensive longitudinal data from annual surveillance reports on resistance and usage in Europe, we find that antibiotic usage in food-producing animals and antibiotic usage in humans are independently and causally related to the prevalence of resistance in both humans and animals. The study considers simultaneous and total usage of antibiotics in humans and food-producing animals to identify the marginal effects and joint effects of usage on resistance of both groups. By employing lagged-dependent variable and fixed-effects specifications, we provide a lower and an upper bound on the effects on resistance. The paper also contributes to the scant literature on how antibiotic use in humans is related to resistance in other animals.

Persistence of Antibiotic Resistance Genes Varies with Particle Size and Substrate Conditions in Recirculating Streams

Antibiotic resistance (AR) determinants are enriched in animal manures, a significant portion of which is land-applied as a soil amendment or as fertilizer, leading to potential AR runoff and microbial pollution in adjacent surface waters. To effectively inform AR monitoring and mitigation efforts, a thorough understanding and description of the persistence and transport of manure-derived AR in flowing waters are needed. We used experimental recirculating mesocosms to assess water-column removal rates of antibiotic resistance genes (ARGs) originating from a cow manure slurry collected from a dairy farm. We quantified the effect of three benthic (i.e., bottom) substrate variations and particle sizes of manure slurry on water column removal rates. Overall, we observed variation in ARG behavior across substrate treatments and particle sizes. For ARGs associated with small particles, removal rates were higher in mesocosms with a substrate. tetW was typically removed at the highest rates across particle size and treatment, followed by ermB and bla_TEM. Our data suggests that both substrate character and particle size exert control on the fate and transport of ARGs in surface waters, laying the foundation for future research in this area to establish a predictive framework for AR persistence and fate in flowing waters.

Metagenomic analysis to determine the characteristics of antibiotic resistance genes in typical antibiotic-contaminated sediments

Comprehensive studies of the effects of various physical and chemical variables (including heavy metals), antibiotics, and microorganisms in the environment on antibiotic resistance genes are rare. We collected sediment samples from the Shatian Lake aquaculture area and surrounding lakes and rivers located in Shanghai, China. The spatial distribution of sediment ARGs was assessed by metagenomic analysis that revealed 26 ARG types (510 subtypes), dominated by Multidrug, β-lactam, Aminoglycoside, Glycopeptides, Fluoroquinolone, and Tetracyline. Redundancy discriminant analysis indicated that antibiotics (SAs and MLs) in the aqueous environment and sediment along with water TN and TP were the key variables affecting the abundance distribution of total ARGs. However, the main environmental drivers and key influences differed among the different ARGs. For total ARGs, the environmental subtypes affecting their structural composition and distribution characteristics were mainly antibiotic residues. Procrustes analysis showed a significant correlation between ARGs and microbial communities in the sediment in the survey area. Network analysis revealed that most of the target ARGs were significantly and positively correlated with microorganisms, and a small number of ARGs (e.g., rpoB, mdtC, and efpA) were highly significantly and positively correlated with microorganisms (e.g., Knoellia, Tetrasphaera, and Gemmatirosa). Potential hosts for the major ARGs included Actinobacteria, Proteobacteria, and Gemmatimonadetes. Our study provides new insight and a comprehensive assessment of the distribution and abundance of ARGs and the drivers of ARG occurrence and transmission.

High-risk antibiotics positively correlated with antibiotic resistance genes in five typical urban wastewater

Antibiotic resistance genes (ARGs) and antibiotic amount increased within close proximity to human dominated ecosystems. However, few studies assessed the distribution of antibiotics and ARGs in multiple ecosystems especially the different urban wastewater. In this study, the spatial distribution of ARGs and antibiotics across the urban wastewater included domestic, livestock, hospital, pharmaceutical wastewater, influent of the wastewater treatment plant (WWTP) in Northeast China. The q-PCR results showed that ARGs were most abundant in community wastewater and followed by WWTP influent, livestock wastewater, pharmaceutical wastewater and hospital wastewater. The ARG composition differed among the five ecotypes with qnrS was the dominant ARG subtypes in WWTP influent and community wastewater, while sul2 dominant in livestock, hospital, pharmaceutical wastewater. The concentration of antibiotics was closely related to the antibiotic usage and consumption data. In addition to the high concentration of azithromycin at all sampling points, more than half of the antibiotics in livestock wastewater were veterinary antibiotics. However, antibiotics that closely related to humankind such as roxithromycin and sulfamethoxazole accounted for a higher proportion in hospital wastewater (13.6%) and domestic sewage (33.6%), respectively. The ambiguous correlation between ARGs and their corresponding antibiotics was detected. However, antibiotics that exhibited high ecotoxic effects were closely and positively correlated with ARGs and the class 1 integrons (intI1), which indicated that high ecotoxic compounds might affect antimicrobial resistance of bacteria by mediating horizontal gene transfer of ARGs. The coupling mechanism between the ecological risk of antibiotics and bacterial resistance needed to be further studied, and thereby provided a new insight to study the impact of environmental pollutants on ARGs in various ecotypes.

Reduced selection for antibiotic resistance in community context is maintained despite pressure by additional antibiotics

Selection for antibiotic resistance at very low antibiotic concentrations has been demonstrated for individual antibiotics in single species experiments. Furthermore, selection in these focal strains is reduced when taking place in complex microbial community context. However, in the environment, bacteria are rarely exposed to single, but rather complex mixtures of selective agents. Here, we explored how the presence of a second selective agent affects selection dynamics between isogenic pairs of focal E. coli strains, differing exclusively in a single resistance determinant, in the absence and presence of a model wastewater community across a gradient of antibiotics. An additional antibiotic that exclusively affects the model wastewater community, but to which the focal strains are resistant to, was chosen as the second selective agent. This allowed exploring how inhibition alters the community's ability to reduce selection. In the presence of the community, the selection coefficient at specific antibiotic concentrations was consistently decreased compared to the absence of the community. While pressure through the second antibiotic significantly decreased the activity and diversity of the community, its ability to reduce selection was consistently maintained at levels comparable to those recorded in absence of the second antibiotic. This indicates that the observed effects of community context on selection dynamics are rather based on competitive or protective effects between the focal strains and a small proportion of bacteria within the community, than on general competition for nutrients. These findings have implications for our understanding of the evolution and selection for multi-drug resistant strains.

Metagenomic next generation sequencing for studying antibiotic resistance genes in the environment

Bacterial antimicrobial resistance (AMR) is a persisting and growing threat to human health. Characterization of antibiotic resistance genes (ARGs) in the environment is important to understand and control ARG-associated microbial risks. Numerous challenges exist in monitoring ARGs in the environment, due to the extraordinary diversity of ARGs, low abundance of ARGs with respect to the complex environmental microbiomes, difficulties in linking ARGs with bacterial hosts by molecular methods, difficulties in achieving quantification and high throughput simultaneously, difficulties in assessing mobility potential of ARGs, and difficulties in determining the specific AMR determinant genes. Advances in the next generation sequencing (NGS) technologies and related computational and bioinformatic tools are facilitating rapid identification and characterization ARGs in genomes and metagenomes from environmental samples. This chapter discusses NGS-based strategies, including amplicon-based sequencing, whole genome sequencing, bacterial population-targeted metagenome sequencing, metagenomic NGS, quantitative metagenomic sequencing, and functional/phenotypic metagenomic sequencing. Current bioinformatic tools for analyzing sequencing data for studying environmental ARGs are also discussed.

Differential dose-response patterns of intracellular and extracellular antibiotic resistance genes under sub-lethal antibiotic exposure

Although antibiotics are one of the most significant factors contributing to the propagation of antibiotic resistance genes (ARGs), studies on the dose-response relationship at sub-lethal concentrations of antibiotics remain scarce, despite their importance for assessing the risks of antibiotics in the environment. In this study, we constructed a series of microcosms to investigate the propagation of intracellular (iARGs) and extracellular (eARGs) ARGs in both water and biofilms when exposed to antibiotics at various concentrations (1-100 μg/L) and frequencies. Results showed that eARGs were more abundant than iARGs in water, while iARGs were the dominant ARGs form in biofilms. eARGs showed differentiated dose-response relationships from iARGs. The abundance of iARGs increased with the concentration of antibiotics as enhanced selective pressure overcame the metabolic burden of antibiotic-resistant bacteria carrying ARGs. However, the abundance of eARGs decreased with increasing antibiotic concentrations because less ARGs were secreted from bacterial hosts at higher concentrations (100 μg/L). Furthermore, combined exposure to two antibiotics (tetracycline & imipenem) showed a synergistic effect on the propagation of iARGs, but an antagonistic effect on the propagation of eARGs compared to exposure to a single antibiotic. When exposed to antibiotic at a fixed total dose, one-time dosing (1 time/10 d) favored the propagation of iARGs, while fractional dosing (5 times /10 d) favored the propagation of eARGs. This study sheds light on the propagation of antibiotic resistance in the environment and can help in assessing the risks associated with the use of antibiotics.

Spatiotemporal distributions of sulfonamide and tetracycline resistance genes and microbial communities in the coastal areas of the Yangtze River Estuary

In this paper, water and sediments were sampled at eight monitoring stations in the coastal areas of the Yangtze River Estuary in summer and autumn 2021. Two sulfonamide resistance genes (sul1 and sul2), six tetracycline resistance genes (tetM, tetC, tetX, tetA, tetO, and tetQ), one integrase gene (intI1), 16 S rRNA genes, and microbial communities were examined and analyzed. Most resistance genes showed relatively higher abundance in summer and lower abundance in autumn. One-way analysis of variance (ANOVA) showed significant seasonal variation of some ARGs (7 ARGs in water and 6 ARGs in sediment). River runoff and WWTPs are proven to be the major sources of resistance genes along the Yangtze River Estuary. Significant and positive correlations between intI1 and other ARGs were found in water samples (P < 0.05), implying that intI1 may influence the spread and propagation of resistance genes in aquatic environments. Proteobacteria was the dominant phylum along the Yangtze River Estuary, with an average proportion of 41.7%. Redundancy analysis indicated that the ARGs were greatly affected by temperature, dissolved oxygen, and pH in estuarine environments. Network analysis showed that Proteobacteria and Cyanobacteria were the potential host phyla for ARGs in the coastal areas of the Yangtze River Estuary.

Microbial community structure and antibiotic resistance profiles in sediments with long-term aquaculture history

The aim of this investigation was to examine the microbial populations and their resistance patterns towards antibiotics, including the impact of nitrogen metabolism in response to the reintroduction of antibiotics, as well as the presence of resistance genes in sediments from shrimp ponds that have been utilized for extended periods of 5, 15, and over 30 years. Results showed that the sediments exhibited a high prevalence of Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, and Oxyphotobacteria as the most abundant bacterial phyla, accounting for 70.35-77.43% of the total bacterial community. The five most abundant phyla of fungi detected in all sediments, namely Rozellomycota, Ascomycota, Aphelidiomycota, Basidiomycota, and Mortierellomycota, constituted 24.26-32.54% of the total fungal community. It was highly probable that the Proteobacteria and Bacteroidetes phyla serve as the primary reservoir of antibiotic-resistant bacteria (ARB) in the sediment, which included various genera like Sulfurovum, Woeseia, Sulfurimonas, Desulfosarcina, and Robiginitalea. Among these genera, Sulfurovum appeared to be the most widespread in the sediment of aquaculture ponds that have been in operation for more than three decades, while Woeseia dominated in ponds that have been recently reclaimed and have a 15-year aquaculture history. Antibiotic resistance genes (ARGs) were categorized into seven distinct groups according to their mechanism of action. The prevalence of multidrug-resistant ARGs was found to be the highest among all types, with an abundance ranging from 8.74 × 10^-2 to 1.90 × 10^-1 copies per 16S rRNA gene copies. The results of a comparative analysis of sediment samples with varying aquaculture histories indicated that the total relative abundance of ARGs was significantly diminished in sediment with a 15-year aquaculture history as opposed to sediment with either a 5-year or 30-year aquaculture history. Another assessment of antibiotic resistances in aquaculture sediments involved an examination of the effects of reintroducing antibiotics on nitrogen metabolism processes. The findings revealed that the rates of ammonification, nitrification, and denitrification in the sediment with a history of 5 years and 15 years, decreased as the concentration of oxytetracycline increased from 1 to 300, and 2000 mg/kg, and inhibitory effects were found to be less pronounced in sediments with a 5-year history compared to those with a 15-year history. In contrast, oxytetracycline exposure led to a significant decrease in the rates of these processes in aquaculture pond sediments with a >30 years of aquaculture history across all the concentrations tested. The emergence and dissemination of antibiotic resistance profiles in aquaculture environments requires attention in future aquaculture management.

Occurrence and influencing factors of antibiotics and antibiotic resistance genes in sediments of the largest multi-habitat lakes in Northern China

Baiyangdian Lake is a typical and largest multi-habitat lake in the North plain of China. To understand the generation and transmission of antibiotics resistance genes (ARGs) in multi-habitat lakes, the contents of nutrients (TC, TOC, TN, TP and TS), heavy metals (Zn, Cr, Ni, Cu, Pb, As, Cd and Hg), 22 antibiotics, 16S-rRNA(16S), Class I integron (intI1) and 20 ARGs were determined. Samples were taken from the Fuhe river, river estuaries, reed marshes, living area, fish ponds and open water of Baiyangdian Lake. The results showed that quinolones were the main pollutants in six habitats, and the content range was ND-104.94 ng/g. Thereinto, aac (6') -IB, blaTEM-1, ermF, qnrA, qnrD, tetG, sul1, sul2 and tetM were detected in all the analyzed samples. The absolute abundance of sul1 was the highest (5.25 × 10⁵ copies/g-6.21 × 10⁷ copies/g) in most of the samples. In these different habitats, the abundance of antibiotics and ARGs in river estuary was the highest, and that in reed marshes was the lowest. There was a significant positive correlation between the abundance of heavy metals (Cu, Pb, Zn, Ni, Cd, Hg) and the absolute abundance of 11 ARGs (P < 0.01). Redundancy analysis showed that Cu, Zn, intI1, TP and macrolides were the important factors affecting the distribution of ARGs. Our finding provides a more likely driving and influencing factor for the transmission of ARGs in lakes with complex and diverse habitats.

A Review of Antibiotics, Antibiotic Resistant Bacteria, and Resistance Genes in Aquaculture: Occurrence, Contamination, and Transmission

Antibiotics are commonly used to prevent and control diseases in aquaculture. However, long-term/overuse of antibiotics not only leaves residues but results in the development of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Antibiotics, ARB, and ARGs are widespread in aquaculture ecosystems. However, their impacts and interaction mechanisms in biotic and abiotic media remain to be clarified. In this paper, we summarized the detection methods, present status, and transfer mechanisms of antibiotics, ARB, and ARGs in water, sediment, and aquaculture organisms. Currently, the dominant methods of detecting antibiotics, ARB, and ARGs are UPLC-MS/MS, 16S rRNA sequencing, and metagenomics, respectively. Tetracyclines, macrolides, fluoroquinolones, and sulfonamides are most frequently detected in aquaculture. Generally, antibiotic concentrations and ARG abundance in sediment are much higher than those in water. Yet, no obvious patterns in the category of antibiotics or ARB are present in organisms or the environment. The key mechanisms of resistance to antibiotics in bacteria include reducing the cell membrane permeability, enhancing antibiotic efflux, and structural changes in antibiotic target proteins. Moreover, horizontal transfer is a major pathway for ARGs transfer, including conjugation, transformation, transduction, and vesiculation. Identifying, quantifying, and summarizing the interactions and transmission mechanisms of antibiotics, ARGs, and ARB would provide useful information for future disease diagnosis and scientific management in aquaculture.

Global Increase of Antibiotic Resistance Genes in Conjugative Plasmids

Antibiotic resistance is propagating worldwide, but the predominant dissemination mechanisms are not fully understood. Here, we report that antibiotic resistance gene (ARG) abundance in conjugative plasmids that are recorded in the National Center for Biotechnology Information (NCBI) RefSeq plasmid database is increasing globally, which is likely a key factor in the propagation of resistance. ARG abundance in plasmids increased by 10-fold on a global scale from the year 2000 to the year 2020 (from 0.25 to 2.93 ARG copies/plasmid), with a more pronounced increase being observed in low-to-middle income countries. This increasing trend of plasmid-borne ARGs was corroborated by bootstrap resampling from each year of the NCBI RefSeq plasmid database. The results of a correlation analysis imply that if antibiotic consumption keeps growing at the current rates, a 2.7-fold global increase in the ARG abundance of clinically relevant plasmids may be reached by 2030. High sequence similarities of clinically relevant, conjugative plasmids that are isolated both from clinics and from the environment raise concerns about the environmental resistome serving as a potential ARG maintenance reservoir that facilitates transmission across these ecological boundaries. IMPORTANCE Antibiotic resistance propagation is a significant concern due to its projected impacts on both global health and the economy. However, global propagation mechanisms are not fully understood, including regional and temporal trends in the abundance of resistance plasmids that facilitate antibiotic resistance gene (ARG) dissemination. This unprecedented study reports that ARG abundance in the conjugative plasmids that are recorded in the National Center for Biotechnology Information (NCBI) database and harbor ARGs is increasing globally with antibiotic consumption, especially in low-to-medium income countries. Through network and comparative genomic analyses, we also found high sequence similarities of clinically relevant conjugative resistance plasmids that were isolated from clinical and environmental sources, suggesting transmission between these ecological boundaries. Therefore, this study informs the One Health perspective to develop effective strategies by which to curtail the propagation of plasmid-borne antibiotic resistance.

Ethiopia's Antibiotic Footprint: Employing the Newly Emerging Digital Concept to Estimate Annual Consumption for the Country

Background The processes involving resistance development against antibiotics have historically been part of the Darwinian evolution. However, the increasing use of antibiotics in modern medicine has intensified the selection pressures with an acute gear-up, rather than as part of this very slow evolutionary process that selects for enhanced fitness for survival. Two major recommendations have been made in the past to tackle this challenge: (1) incentivizing the pharmaceutical industry to invest more in research and development endeavors so that they come up with new antibiotics, and (2) implementing antimicrobial stewardship programs in healthcare systems. Methodology In this study, the third and emerging approach, namely, documenting antibiotic footprint, was employed as a communication tool that targets individual consumers of antibiotics. Data obtained from the Ethiopian Pharmaceutical Supply Agency were curated to systematically compile antibiotic consumption at each of the agency's regional hubs. The exact geospatial locations of the hubs were generated and synchronized to depict the size of the antibiotic footprint infograph as proportional to the antibiotic consumption data at each hub. Moreover, the cumulative and per-capita consumption of these antibiotics at the country level (overall antibiotic footprint) were calculated by including estimated data for the livestock sector. Results A total of 698.2 tons of antibiotics were used in Ethiopia in 2018, and the per-capita consumption of antibiotics was 5.8 g per person. Extended-spectrum (J01CA) and beta-lactamase-resistant penicillins (J01CF) were the most commonly utilized classes of antibiotics which accounted for, respectively, 38.3% and 20.8% of all antibiotics used in the country's public health sector. Hubs in Addis Ababa (14%) and Hawassa (12%) topped the overall antibiotic consumption in the country. Contrarily, hubs in Gambella and Semera received relatively smaller quantities of antibiotics, with totals of 4.8 tons (0.9%) and 10.2 tons (1.9%), respectively. Conclusions This study shows that the newly emerging concept of the antibiotic footprint is a simple and suitable tool for public health policy communications targeting individual consumers of antibiotics. If implemented judicially, the concept of the antibiotic footprint has a huge potential to support global scientific efforts and collaborations in setting standards that help to reduce the overuse and misuse of antibiotics in the future.

Bacterial inactivation processes in water disinfection - mechanistic aspects of primary and secondary oxidants - A critical review

Water disinfection during drinking water production is one of the most important processes to ensure safe drinking water, which is gaining even more importance due to the increasing impact of climate change. With specific reaction partners, chemical oxidants can form secondary oxidants, which can cause additional damage to bacteria. Cases in point are chlorine dioxide which forms free available chlorine (e.g., in the reaction with phenol) and ozone which can form hydroxyl radicals (e.g., during the reaction with natural organic matter). The present work reviews the complex interplay of all these reactive species which can occur in disinfection processes and their potential to affect disinfection processes. A quantitative overview of their disinfection strength based on inactivation kinetics and typical exposures is provided. By unifying the current data for different oxidants it was observable that cultivated wild strains (e.g., from wastewater treatment plants) are in general more resistant towards chemical oxidants compared to lab-cultivated strains from the same bacterium. Furthermore, it could be shown that for selective strains chlorine dioxide is the strongest disinfectant (highest maximum inactivation), however as a broadband disinfectant ozone showed the highest strength (highest average inactivation). Details in inactivation mechanisms regarding possible target structures and reaction mechanisms are provided. Thereby the formation of secondary oxidants and their role in inactivation of pathogens is decently discussed. Eventually, possible defense responses of bacteria and additional effects which can occur in vivo are discussed.

Meta-analysis addressing the characterization and risk identification of antibiotics and antibiotic resistance genes in global groundwater

Antimicrobial resistance (AMR) is one of the significant global issues to public health. Compared to other aquatic environments, research on AMR in groundwater is scarce. In the study, a meta-analysis was conducted to explore the characteristics and risks of antibiotics and antibiotic resistance genes (ARGs) in global groundwater, using a data set of antibiotic concentrations collected from publications during 2000-2021 and a large-scale metagenomes of groundwater samples (n = 330). The ecotoxicological risks of antibiotics in the global groundwater were evaluated using mixture risk quotient with concentration addition model to consider the synergistic effects of multiple antibiotics. Bioinformatic annotations identified 1413 ARGs belonging to 37 ARG types in the global groundwater, dominated by rifamycin, polyketide, and quinolone resistance genes and including some emerging ARGs such as mcr-family and carbapenem genes. Relatively, the level of ARGs in the groundwater from spring was significantly higher (ANOVA, p < 0.01) than those from the riparian zone, sand and deep aquifer. Similarly, metal resistance genes (MRGs) were prevalent in the global groundwater, and network analysis suggested the MRGs presented non-random co-occurrence with the ARGs in such environments. Taxonomic annotations showed Proteobacteria, Actinobacteria, Eukaryota, Acidobacteria and Thaumarchaeota were the dominant phylum in the groundwater, and the microbial community largely shaped profile of ARGs in the environment. Notably, the ARGs presented co-occurrence with mobile genetic elements, virulence factors and human bacterial pathogens, indicating potential dissemination risk of ARGs in the groundwater. Furthermore, an omics-based approach was used for health risk assessment of antibiotic resistome and screened out 152 risk ARGs in the global groundwater. Comparatively, spring and cold creek presented higher risk index, which deserves more attention to ensure the safety of water supply.

Emerging soil contamination of antibiotics resistance bacteria (ARB) carrying genes (ARGs): New challenges for soil remediation and conservation

Soil plays a vital role as a nutrient source for microflora and plants in ecosystems. The accumulation and proliferation of antibiotics resistance bacteria (ARB) and antibiotics resistance genes (ARGs) causes emerging soil contamination and pollution, posing new challenges for soil remediation, recovery, and conservation. Fertilizer application in agriculture is one of the most important sources of ARB and ARGs contamination in soils. The recent existing techniques for the remediation of soil polluted with ARB and ARGs are very limited in terms of ARB and ARGs removal in soil. Bioelectrochemical remediation using bioelectrochemical systems such as microbial fuel cells and microbial electrolysis cells are promising technologies for the removal of ARB and ARGs in soil. Herein, diverse sources of ARB and ARGs in soil have been reviewed, their effects on soil microbial diversity have been analyzed, and the causes of ARB and ARGs rapid proliferation in soil are explained. Bioelectrochemical systems used for the remediation of soil contaminated with ARB and ARGs is still in its infancy stage and presents serious disadvantage and limits, therefore it needs to be well understood and implemented. In general, merging soil contamination of ARB and ARGs is an increasing concern threatening the soil ecosystem while the remediation technologies are still challenging. Efforts need to be made to develop new, effective, and efficient technologies for soil remediation and conservation to tackle the spread of ARB and ARGs and overcome the new challenges posed by ARB and ARGs contamination in soil.

Global profiling of antibiotic resistomes in maize rhizospheres

The spreading of antimicrobial resistance (AMR) in crops and food products represents a global concern. In this study, we conducted a survey of resistomes in maize rhizosphere from Michigan, California, the Netherlands, and South Africa, and investigated potential associations with host bacteria and soil management practices in the crop field. For comparison, relative abundance of antibiotic resistance genes (ARGs) is normalized to the size of individual metagenomes. Michigan maize rhizosphere metagenomes showed the highest abundance and diversity of ARGs, with the detection of blaTEM-116, blaACT-4/-6, and FosA2, exhibiting high similarity (≥ 99.0%) to those in animal and human pathogens. This was probably related to the decade-long application of manure/composted manure from antibiotic-treated animals. Moreover, RbpA, vanRO, mtrA, and dfrB were prevalently found across most studied regions, implying their intrinsic origins. Further analysis revealed that RbpA, vanRO, and mtrA are mainly harbored by native Actinobacteria with low mobility since mobile genetic elements were rarely found in their flanking regions. Notably, a group of dfrB genes are adjacent to the recombination binding sites (attC), which together constitute mobile gene cassettes, promoting the transmission from soil bacteria to human pathogens. These results suggest that maize rhizosphere resistomes can be distinctive and affected by many factors, particularly those relevant to agricultural practices.

Soil antibiotic resistance genes accumulate at different rates over four decades of manure application

Manure can be a source of antibiotic resistance genes (ARGs) that enter the soil. However, previous studies assessing ARG persistence in soil have generally lacked continuity over sampling times, consistency of location, and assessing the impact of discontinuing manure application. We evaluated both short- and long-term ARG accumulation dynamics in soil with a 40-year known history of manure use. Manure application caused a greater abundance of tetracycline, macrolide, and sulfonamide ARGs in the soil. There was an initial spike in ARG abundance resulting from manure bacteria harboring ARGs being introduced to soil, followed by resident soil bacteria out-competing them, which led to ARG dissipation within a year. However, over four decades, annual manure application caused linear or exponential ARG accumulation, and bacteria associated with ARGs differed compared to those in the short term. Eleven years after discontinuing manure application, most soil ARG levels declined but remained elevated. We systematically explored the historical accumulation of ARGs in manured soil, and provide insight into factors that affect their persistence.

Phytostabilization mitigates antibiotic resistance gene enrichment in a copper mine tailings pond

Mining-impacted environments are distributed globally and have become increasingly recognized as hotspots of antibiotic resistance genes (ARGs). However, there are currently no reports on treatment technologies to deal with such an important environmental problem. To narrow this knowledge gap, we implemented a phytostabilization project in an acidic copper mine tailings pond and employed metagenomics to explore ARG characteristics in the soil samples. Our results showed that phytostabilization decreased the total ARG abundance in 0-10 cm soil layer by 75 %, which was companied by a significant decrease in ARG mobility, and a significant increase in ARG diversity and microbial diversity. Phytostabilization was also found to drastically alter the ARG host composition and to significantly reduce the total abundance of virulence factor genes of ARG hosts. Soil nutrient status, heavy metal toxicity and SO₄^2- concentration were important physicochemical factors to affect the total ARG abundance, while causal mediation analysis showed that their effects were largely mediated by the changes in ARG mobility and microbial diversity. The increase in ARG diversity associated with phytostabilization was mainly mediated by a small subgroup of ARG hosts, most of which could not be classified at the genus level and deserve further research in the future.

Soil Component: A Potential Factor Affecting the Occurrence and Spread of Antibiotic Resistance Genes

In recent years, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil have become research hotspots in the fields of public health and environmental ecosystems, but the effects of soil types and soil components on the occurrence and spread of ARGs still lack systematic sorting and in-depth research. Firstly, investigational information about ARB and ARGs contamination of soil was described. Then, existing laboratory studies about the influence of the soil component on ARGs were summarized in the following aspects: the influence of soil types on the occurrence of ARGs during natural or human activities and the control of exogenously added soil components on ARGs from the macro perspectives, the effects of soil components on the HGT of ARGs in a pure bacterial system from the micro perspectives. Following that, the similarities in pathways by which soil components affect HGT were identified, and the potential mechanisms were discussed from the perspectives of intracellular responses, plasmid activity, quorum sensing, etc. In the future, related research on multi-component systems, multi-omics methods, and microbial communities should be carried out in order to further our understanding of the occurrence and spread of ARGs in soil.